scholarly journals Hiding in plain sight: DNA barcoding suggests cryptic species in all ‘well-known’ Australian flower beetles (Scarabaeidae: Cetoniinae)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9348
Author(s):  
Andrew Mitchell ◽  
Christian H. Moeseneder ◽  
Paul M. Hutchinson
Keyword(s):  
Cryptic Species ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Undescribed Species ◽  
Species Discovery ◽  
Multiple Clusters ◽  
High Diversity

DNA barcode data is presented for Australian cetoniine flower beetles to aid with species discovery and guide revisionary taxonomy. Sequences of the COI gene’s DNA barcode region were acquired from 284 cetoniine specimens, covering 68 described species and 33 genera. This equates to 48% of the known species and 83% of the genera which occur in Australia. Results suggest up to 27 putative undescribed species in our sample, only 11 of which were suspected to be undescribed before this study, leaving 16 unexpected (“cryptic”) species. The Australian cetoniine fauna may hence be increased by up to 19%. An unanticipated result of the work is that each of the five most visible and commonly collected Australian cetoniine species, Eupoecila australasiae (Donovan, 1805), Neorrhina punctatum (Donovan, 1805), Glycyphana (Glycyphaniola) stolata (Fabricius, 1781), Chondropyga dorsalis (Donovan, 1805) and Bisallardiana gymnopleura (Fischer, 1823), have unexpectedly high diversity in DNA barcode sequences and were consequently split into multiple clusters, possibly indicating the presence of cryptic species.

scholarly journals Shrunken Life: Discourses of the Cryptic and the Miniature in Madagascar

2021 ◽  
Vol 20 (2) ◽  
pp. 55-73 ◽  
Author(s):  
Genese Marie Sodikoff
Keyword(s):  
Climate Change ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Habitat Loss ◽  
Physical World ◽  
Species Discovery ◽  
The Public ◽  
Micro Scale ◽  
The World ◽  
Public Imagination

As scientists scour remnant habitats and “unmask” cryptic species with DNA barcoding, a boom of species discovery has enchanted the world.  In Madagascar, recent discoveries of previously unknown miniature frogs, chameleons, and lemurs often photographed on human fingers or cradled in hands, have captured the public imagination. In this imagery of scale, the giant finger conveys the outsized impact of humanity on Earth, or points to what Susan Stewart (1996, p. 74) calls “a physical world of disorder and disproportion.” Although the phenomenon of insular gigantism and dwarfism has shaped scientific discourses of evolution and extinction since the nineteenth century, recent reportage on “new” miniature and cryptic species reflects a sensibility beyond wistful nostalgia for creatures past. Species miniaturism evolves out of habitat loss, and living minifauna encapsulate the contraction of existential time, all the more pronounced by the effects of climate change. Photographs of cryptic minifauna therefore compel us to reflect on the whole of our losses, while they fuel the impulse to restock the “library of life” at micro-scale.  

scholarly journals DNA barcoding of commercially important reef fishes in Weh Island, Aceh, Indonesia

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9641 ◽  
Author(s):  
Nur Fadli ◽  
Siti Azizah Mohd Nor ◽  
Ahmad Sofiman Othman ◽  
Hizir Sofyan ◽  
Zainal A. Muchlisin
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Reef Fishes ◽  
Morphological Identification ◽  
Species Discovery ◽  
Indonesian Archipelago ◽  
Aceh Province ◽  
Commercially Important ◽  
Catch Composition ◽  
Fisheries Statistics

Knowledge on the precise identification of fish resources is critical for sustainable fisheries management. This study employs the DNA barcoding approach to generate a molecular taxonomic catalogue of commercially important reef fishes in the waters of Weh Island (Aceh Province), the most northerly inhabited island in the biodiverse Indonesian Archipelago. The waters not only support artisanal fisheries but also a feeder for the industry in the greater island of Aceh. In total, 230 specimens from 72 species belonging to 32 genera and 17 families were DNA barcoded, representing a major segment of the captured reef fish taxa and a quarter of fish species diversity that had previously been recorded. The sequence read lengths were 639 bp revealing 359 conserved sites, 280 variable sites, 269 parsimony informative and 11 singletons. Our molecular findings paralleled the morphological identification with no evidence of cryptic species or new species discovery. This study is a significant contribution to the fisheries statistics of this area, which would facilitate assessment of species catch composition and hence for strategizing management plans. It is an important input to the DNA barcode library of Indonesian marine fishes and to the global DNA barcode entries in general.

DNA barcoding the Lepidoptera inventory of a large complex tropical conserved wildland, Area de Conservacion Guanacaste, northwestern Costa Rica

Genome ◽  
2016 ◽  
Vol 59 (9) ◽  
pp. 641-660 ◽  
Author(s):  
Daniel H. Janzen ◽  
Winnie Hallwachs
Keyword(s):  
Costa Rica ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Species Level ◽  
Data Systems ◽  
Species Discovery ◽  
Life Data ◽  
And Behavior ◽  
Specimen Identification ◽  
Biodiversity Information

The 37-year ongoing inventory of the estimated 15 000 species of Lepidoptera living in the 125 000 terrestrial hectares of Area de Conservacion Guanacaste, northwestern Costa Rica, has DNA barcode documented 11 000+ species, and the simultaneous inventory of at least 6000+ species of wild-caught caterpillars, plus 2700+ species of parasitoids. The inventory began with Victorian methodologies and species-level perceptions, but it was transformed in 2004 by the full application of DNA barcoding for specimen identification and species discovery. This tropical inventory of an extraordinarily species-rich and complex multidimensional trophic web has relied upon the sequencing services provided by the Canadian Centre for DNA Barcoding, and the informatics support from BOLD, the Barcode of Life Data Systems, major tools developed by the Centre for Biodiversity Genomics at the Biodiversity Institute of Ontario, and available to all through couriers and the internet. As biodiversity information flows from these many thousands of undescribed and often look-alike species through their transformations to usable product, we see that DNA barcoding, firmly married to our centuries-old morphology-, ecology-, microgeography-, and behavior-based ways of taxonomizing the wild world, has made possible what was impossible before 2004. We can now work with all the species that we find, as recognizable species-level units of biology. In this essay, we touch on some of the details of the mechanics of actually using DNA barcoding in an inventory.

DNA-barcoding of sympatric species of ectoparasitic gastropods of the genusCerithiopsis(Mollusca: Gastropoda: Cerithiopsidae) from Croatia

2012 ◽  
Vol 93 (4) ◽  
pp. 1059-1065 ◽  
Author(s):  
M.V. Modica ◽  
P. Mariottini ◽  
J. Prkić ◽  
M. Oliverio
Keyword(s):  
Cryptic Species ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Genetic Data ◽  
Distinct Species ◽  
Sympatric Species ◽  
Species Level ◽  
Colour Pattern ◽  
Coi Sequences

The ectoparasitic gastropod genusCerithiopsisForbes & Hanley, 1850 was nominally based onMurex tubercularisMontagu, 1803. We have used the DNA barcode COI sequences to assay sympatric samples of morphotypes recently described as distinct species of theCerithiopsis tubercularis-complex. Our results demonstrated that, in the Croatian waters, the gastropods usually calledC. tubercularisin fact comprise a complex of cryptic species, which can be reliably diagnosed only by examining the soft parts. In the present study we have demonstrated that the colour pattern of the head-foot is diagnostic at the species level in this complex and, coupled with genetic data, may provide a sounding base for a revision of the cerithiopsids of the European coasts.

scholarly journals DNA Barcoding of Mullets (Family Mugilidae) from Pakistan Reveals Surprisingly High Number of Unknown Candidate Species

Diversity ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 232
Author(s):  
Ariba Hasan ◽  
Pirzada Jamal Ahmed Siddiqui ◽  
Shabir Ali Amir ◽  
Jean-Dominique Durand
Keyword(s):  
Species Diversity ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Morphological Examination ◽  
Operational Taxonomic Units ◽  
Phylogenetic Studies ◽  
Management Measures ◽  
Morphological Criteria ◽  
Candidate Species

The mullets are a widespread group of ecologically and economically important fishes of disputed taxonomy due to their uniform external morphology. Barcoding and phylogenetic studies from various locations around the world largely highlighted the species diversity underestimation using morphological criteria used to establish the taxonomy of the family. Here, we investigated the mullet species diversity from Pakistan, a biogeographic area where nearly no mullet species were genetically characterized. Morphological examination of 40 mullets reveals 6 known species (Planiliza macrolepis, P. klunzingeri, P. subviridis, Crenimugil seheli, Ellochelon vaigiensis, and Mugil cephalus). Using a references DNA barcode library, the DNA barcode-based species identification flagged eight molecular operational taxonomic units (MOTUs) belonging to five genera (Crenimugil, Ellochelon, Mugil, Osteomugil, and Planiliza). Among these MOTUs, only one was already present in Barcode of Life Data system, all other representing new Barcode Index Numbers (BIN). These results emphasize the importance of the recognition of cryptic species and the necessity to re-evaluate the overall diversity by the genetic characterization of different species of this family. DNA barcoding is an effective tool to reveal cryptic species that need to be considered in conservation and management measures of fisheries in Pakistan.

scholarly journals Identification of Indian Spiders through DNA barcoding: Cryptic species and species complex

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kaomud Tyagi ◽  
Vikas Kumar ◽  
Shantanu Kundu ◽  
Avas Pakrashi ◽  
Priya Prasad ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Genetic Distances ◽  
Pairwise Distance ◽  
Global Database ◽  
Species Discovery ◽  
Operational Taxonomic Units ◽  
Tree Topologies ◽  
Multiple Species

Abstract Spiders are mega diverse arthropods and play an important role in the ecosystem. Identification of this group is challenging due to their cryptic behavior, sexual dimorphism, and unavailability of taxonomic keys for juveniles. To overcome these obstacles, DNA barcoding plays a pivotal role in spider identification throughout the globe. This study is the first large scale attempt on DNA barcoding of spiders from India with 101 morphospecies of 72 genera under 21 families, including five endemic species and holotypes of three species. A total of 489 barcodes was generated and analyzed, among them 85 novel barcodes of 22 morphospecies were contributed to the global database. The estimated delimitation threshold of the Indian spiders was 2.6% to 3.7% K2P corrected pairwise distance. The multiple species delimitation methods (BIN, ABGD, GMYC and PTP) revealed a total of 107 molecular operational taxonomic units (MOTUs) for 101 morphospecies. We detected more than one MOTU in 11 morphospecies with discrepancies in genetic distances and tree topologies. Cryptic diversity was detected in Pardosa pusiola, Cyclosa spirifera, and Heteropoda venatoria. The intraspecies distances which were as large as our proposed delimitation threshold were observed in Pardosa sumatrana, Thiania bhamoensis, and Cheiracanthium triviale. Further, shallow genetic distances were detected in Cyrtophora cicatrosa, Hersilia savignyi, Argiope versicolor, Phintella vittata, and Oxyopes birmanicus. Two morphologically distinguished species (Plexippus paykulli and Plexippus petersi) showed intra-individual variation within their DNA barcode data. Additionally, we reinstate the original combination for Linyphia sikkimensis based on both morphology and DNA barcoding. These data show that DNA barcoding is a valuable tool for specimen identification and species discovery of Indian spiders.

DNA barcoding the bees (Hymenoptera: Apoidea) of Chile: species discovery in a reasonably well known bee fauna with the description of a new species of Lonchopria (Colletidae)

Genome ◽  
2017 ◽  
Vol 60 (5) ◽  
pp. 414-430 ◽  
Author(s):  
Laurence Packer ◽  
Luisa Ruz
Keyword(s):  
New Species ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Morphological Differentiation ◽  
Spanish Language ◽  
Dna Barcodes ◽  
Species Discovery ◽  
Traditional Taxonomy ◽  
Taxonomic Research ◽  
A New Species

We compare the diversity of bees in the Chilean fauna as understood from traditional taxonomy-based catalogues with that currently known from DNA barcodes using the BIN system informed by ongoing morphology-based taxonomic research. While DNA barcode surveys of the Chilean bee fauna remain incomplete, it is clear that new species can readily be distinguished using this method and that morphological differentiation of distinct barcode clusters is sometimes very easy. We assess the situation in two genera in some detail. In Lonchopria Vachal one “species” is readily separable into two BINs that are easily differentiated based upon male mandibular and genitalic morphology (characters generally used in this group) as well as female hair patterns. Consequently, we describe Lonchopria (Lonchopria) heberti Packer and Ruz, new species. For Liphanthus Reed, a large number of new species has been detected using DNA barcoding and considerable additional traditional morphological work will be required to describe them. When we add the number of BINs (whether identified to named species or not) to the number of Chilean bee species that we know have not been barcoded (both described and new species under study in our laboratories) we conclude that the bee fauna of Chile is substantially greater than the 436 species currently known. Spanish language abstract available as supplementary data 1 .

scholarly journals Differentiation of Mitragyna speciosa, a narcotic plant, from allied Mitragyna species using DNA barcoding-high-resolution melting (Bar-HRM) analysis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chayapol Tungphatthong ◽  
Santhosh Kumar J. Urumarudappa ◽  
Supita Awachai ◽  
Thongchai Sooksawate ◽  
Suchada Sukrong
Keyword(s):  
High Resolution ◽  
Dna Barcoding ◽  
High Resolution Melting ◽  
Dna Barcode ◽  
Herbal Medicines ◽  
Efficient Tool ◽  
Hrm Analysis ◽  
Mitragyna Speciosa ◽  
Leaf Powder

AbstractMitragyna speciosa (Korth.) Havil. [MS], or “kratom” in Thai, is the only narcotic species among the four species of Mitragyna in Thailand, which also include Mitragyna diversifolia (Wall. ex G. Don) Havil. [MD], Mitragyna hirsuta Havil. [MH], and Mitragyna rotundifolia (Roxb.) O. Kuntze [MR]. M. speciosa is a tropical tree belonging to the Rubiaceae family and has been prohibited by law in Thailand. However, it has been extensively covered in national and international news, as its abuse has become more popular. M. speciosa is a narcotic plant and has been used as an opium substitute and traditionally used for the treatment of chronic pain and various illnesses. Due to morphological disparities in the genus, the identification of plants in various forms, including fresh leaves, dried leaf powder, and finished products, is difficult. In this study, DNA barcoding combined with high-resolution melting (Bar-HRM) analysis was performed to differentiate M. speciosa from allied Mitragyna and to assess the capability of Bar-HRM assays to identify M. speciosa in suspected kratom or M. speciosa-containing samples. Bar-HRM analysis of PCR amplicons was based on the ITS2, rbcL, trnH-psbA, and matK DNA barcode regions. The melting profiles of ITS2 amplicons were clearly distinct, which enabled the authentication and differentiation of Mitragyna species from allied species. This study reveals that DNA barcoding coupled with HRM is an efficient tool with which to identify M. speciosa and M. speciosa-containing samples and ensure the safety and quality of traditional Thai herbal medicines.

scholarly journals Benchmarking DNA barcodes: an assessment using available primate sequences

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 851-854 ◽  
Author(s):  
Mehrdad Hajibabaei ◽  
Gregory AC Singer ◽  
Donal A Hickey
Keyword(s):  
New Species ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Primate Species ◽  
Dna Barcodes ◽  
Global Biodiversity ◽  
Efficient Sequence

DNA barcoding has been recently promoted as a method for both assigning specimens to known species and for discovering new and cryptic species. Here we test both the potential and the limitations of DNA barcodes by analysing a group of well-studied organisms—the primates. Our results show that DNA barcodes provide enough information to efficiently identify and delineate primate species, but that they cannot reliably uncover many of the deeper phylogenetic relationships. Our conclusion is that these short DNA sequences do not contain enough information to build reliable molecular phylogenies or define new species, but that they can provide efficient sequence tags for assigning unknown specimens to known species. As such, DNA barcoding provides enormous potential for use in global biodiversity studies.Key words: DNA barcoding, species identification, primate, biodiversity.

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